title: Reticulate evolution of the rye genome.
abstract: Rye (Secale cereale) is closely related to wheat (Triticum aestivum) and barley (Hordeum vulgare). Due to its large genome (~8 Gb) and its regional importance, genome analysis of rye has lagged behind other cereals. Here, we established a virtual linear gene order model (genome zipper) comprising 22,426 or 72% of the detected set of 31,008 rye genes. This was achieved by high-throughput transcript mapping, chromosome survey sequencing, and integration of conserved synteny information of three sequenced model grass genomes (Brachypodium distachyon, rice [Oryza sativa], and sorghum [Sorghum bicolor]). This enabled a genome-wide high-density comparative analysis of rye/barley/model grass genome synteny. Seventeen conserved syntenic linkage blocks making up the rye and barley genomes were defined in comparison to model grass genomes. Six major translocations shaped the modern rye genome in comparison to a putative Triticeae ancestral genome. Strikingly dissimilar conserved syntenic gene content, gene sequence diversity signatures, and phylogenetic networks were found for individual rye syntenic blocks. This indicates that introgressive hybridizations (diploid or polyploidy hybrid speciation) and/or a series of whole-genome or chromosome duplications played a role in rye speciation and genome evolution.
authors.affiliation: Helmholtz Center Munich, German Research Centre for Environmental Health, Munich Information Center for Protein Sequences/IBIS, Institute of Bioinformatics and Systems Biology, 85764 Neuherberg, Germany.
authors.forename: Mihaela M
authors.initials: MM
authors.lastname: Martis
authors.forename: Ruonan
authors.initials: R
authors.lastname: Zhou
authors.forename: Grit
authors.initials: G
authors.lastname: Haseneyer
authors.forename: Thomas
authors.initials: T
authors.lastname: Schmutzer
authors.forename: Jan
authors.initials: J
authors.lastname: Vrána
authors.forename: Marie
authors.initials: M
authors.lastname: Kubaláková
authors.forename: Susanne
authors.initials: S
authors.lastname: König
authors.forename: Karl G
authors.initials: KG
authors.lastname: Kugler
authors.forename: Uwe
authors.initials: U
authors.lastname: Scholz
authors.forename: Bernd
authors.initials: B
authors.lastname: Hackauf
authors.forename: Viktor
authors.initials: V
authors.lastname: Korzun
authors.forename: Chris-Carolin
authors.initials: CC
authors.lastname: Schön
authors.forename: Jaroslav
authors.initials: J
authors.lastname: Dolezel
authors.forename: Eva
authors.initials: E
authors.lastname: Bauer
authors.forename: Klaus F X
authors.initials: KF
authors.lastname: Mayer
authors.forename: Nils
authors.initials: N
authors.lastname: Stein
mesh_terms: D058431:Brachypodium / Q000235:genetics; D002874:Chromosome Mapping; D032461:Chromosomes, Plant; D017124:Conserved Sequence; D018744:DNA, Plant / Q000235:genetics; D019143:Evolution, Molecular; D023061:Gene Order; D049810:Genetic Speciation; D018745:Genome, Plant; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D001467:Hordeum / Q000235:genetics; D008957:Models, Genetic; D012275:Oryza / Q000235:genetics; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D012434:Secale / Q000235:genetics*; D017422:Sequence Analysis, DNA; D026801:Synteny
chemical_list: D018744:DNA, Plant